Package: occumb 1.1.0.9012

occumb: Site Occupancy Modeling for Environmental DNA Metabarcoding

Fits multispecies site occupancy models to environmental DNA metabarcoding data collected using spatially-replicated survey design. Model fitting results can be used to evaluate and compare the effectiveness of species detection to find an efficient survey design. Reference: Fukaya et al. (2022) <doi:10.1111/2041-210X.13732>.

Authors:Keiichi Fukaya [aut, cre], Ken Kellner [cph], Mika Takahashi [aut]

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occumb.pdf |occumb.html✨
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NEWS

# Install 'occumb' in R:
install.packages('occumb', repos = c('https://fukayak.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fukayak/occumb/issues

Pkgdown site:https://fukayak.github.io

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:
  • fish - Fish eDNA metabarcoding dataset
  • fish_raw - Fish eDNA metabarcoding dataset

On CRAN:

Conda:

jagscpp

5.30 score 2 stars 10 scripts 233 downloads 12 exports 12 dependencies

Last updated 2 months agofrom:19bf99b504. Checks:6 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 27 2025
R-4.5-winNOTEMar 27 2025
R-4.5-macNOTEMar 27 2025
R-4.5-linuxNOTEMar 27 2025
R-4.4-winOKMar 27 2025
R-4.4-macOKMar 27 2025
R-4.4-linuxOKMar 27 2025
R-4.3-winOKMar 27 2025
R-4.3-macOKMar 27 2025

Exports:eval_util_Leval_util_Rget_post_samplesget_post_summarygoflist_cond_Llist_cond_RoccumboccumbDataplotpredictsummary

Dependencies:backportscheckmatecodacrayonevaluatehighrjagsUIknitrlatticerjagsxfunyaml

Introduction to occumb

Rendered fromoccumb.Rmdusingknitr::rmarkdownon Mar 27 2025.

Last update: 2024-11-05
Started: 2023-07-20

Model specification in occumb()

Rendered frommodel_specification.Rmdusingknitr::rmarkdownon Mar 27 2025.

Last update: 2024-03-08
Started: 2023-07-20